Hi Ettore.
Comments below. > I have the following question. In the "sup3.R" file the probe level > model fitting is realised using the instructions: > > plm <- RmaPlm(csNU) > fit(plm, verbose=verbose) > > where csNU is an object obtained after background correction, quantile > normalisation and conversion of the cdf to a "unique" version. The conversion to 'unique' is actually done both on the CDF and the data. This is simply to dance around the fact that a handful of probes are used in multiple probesets. > I suppose that this approach should enable the exon-level analysis of > the Gene 1.0 data, as required by FIRMAGene. However I don't > understand where is the difference since the methods are the same as > in the gene-level analysis of such data. I'm actually not sure what it is you are asking here. Indeed, the methodology of FIRMAGene operates on the results (specifically, the residuals) of your standard RMA probe level model. This is, however, quite different to the standard DE analysis, if that is what you mean by "gene-level analysis". Hope that helps. Cheers, Mark > > Thanks, > > > Ettore M. > > > On May 29, 3:16 pm, rhizomorph <cognitiontechnic...@yahoo.com> wrote: >> I have the same question as Ettore. I installed the aroma.affymetrix >> package (and all supporting packages), but nowhere can I find a source >> to download and install the FIRMAGene package that the "SUP3.R" script >> clearly calls for. >> >> Rhizomorph. >> >> On May 29, 3:15 am, ettore mosca <ettore.mos...@gmail.com> wrote: >> >> > Dear aroma.affymetrix developers, >> >> > I'm very interested in using Gene 1.0 ST platform for alternative >> > splicing. I read in your paper "Differential splicing using >> > whole-transcript microarrays" that FIRMAGene "is freely available as R >> > package" but I can not load the library following the instruction in >> the >> > third additional file "sup3.r" (I installed and loaded >> aroma.affymetrix >> > successfully) >> >> > How do I install and load FIRMAGene library? >> >> > Thanks, >> >> > Ettore M. >> >> > -- >> > Ettore M. >> >> >http://www.ettoremosca.it > > > --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
